I find I'm doing far better now. While I was respecing to make full use of the plasmonic console I also noticed I didn't have a single point in armor reinforcements. I sunk 5 in there and between that and the 17 energy to all systems I'm getting out of the console, my survival issues are basically solved. After I have enough zen to get the valdore console it'll be roflstomping time.

As stated previously, if you put your build, it's easier to help.
However, to me there is one or two things you need to learn with the Scimitar; plan ahead and don't push it. Fire, go away (cloak), go at it again, etc...

The scimitar is no bigger than the bortasqu or dread carrier. In fact it plays almost identically to them. It is mainly different due to aesthetics. Best advice to the op. Find the energy type you prefer. And build yourself around it. Flag ships especially in PvP are prone to being the primary targets. Because they can muscle out of a fight better most of the time.

Despite how much before LOR release ferasian shadow force got on my ass how they so strongly believed the scimitar would never be released.....

Overall I feel the scim isn't as fun as my bort. But that's OK. The key to flying the flagships right. Is knowing when to pull out or redirect to another target.

Find Bortasqu/Dread Carrier pilots who can survive and fight decently, if not really good in PVP in them, and have them show you how to manuver and work with such massive ships. The real beater the flag ships really is their size. But get a fleet/group of them, you can pave a path in any group of Escorts/BoPs without much issues. So long as you're coordinated.

the scimitar can battlecloack with shields up. so do it. then decloack and take the longer lasting damage and defense buff with you on your rapid/scatter and or BO attack.
and why not drop mines too. they do the damage they had listed when they got dropped. . .

hey btw the phase cloack from the dorkidex retrofit allows the use of the thalaron gun.

and you can add the shield heal proc console. just how are you die ing again?